Daigo Kobayashi loses his job as a cellist when his orchestra is disbanded. He and his wife Mika move from Tokyo to his hometown in Yamagata, where they live in his childhood home that was left to him when his mother died two years earlier. It is fronted by a coffee shop that Daigo's father had operated before he ran off with a waitress when Daigo was six; since then the two have had no contact. Daigo feels hatred towards his father and guilt for not taking better care of his mother. He still keeps a "stone-letter" - a stone which is said to convey meaning through its texture - which his father had given him many years before.
Daigo finds an advertisement for a job "assisting departures". Assuming it to be a job in a travel agency, he goes to the interview at the NK Agent office and learns from the secretary, Yuriko Kamimura, that he will be preparing bodies for cremation in a ceremony known as encoffinment. Though reluctant, Daigo is hired on the spot and receives a cash advance from his new boss, Sasaki. Daigo is furtive about his duties and hides the true nature of the job from Mika.
His first assignment is to assist with the encoffinment of a woman who died at home and remained undiscovered for two weeks. He is beset with nausea and later humiliated when strangers on a bus detect an unsavoury scent on him. To clean himself, he visits a public bath which he had frequented as a child. It is owned by Tsuyako Yamashita, the mother of one of Daigo's former classmates.
Over time, Daigo becomes comfortable with his profession as he completes a number of assignments and experiences the gratitude of the families of the deceased. Though he faces social ostracism, Daigo refuses to quit, even after Mika discovers a training DVD in which he plays a corpse and leaves him to return to her parents' home in Tokyo. Daigo's former classmate Yamashita insists that the mortician find a more respectable line of work and, until then, avoids him and his family.
After a few months, Mika returns and announces that she is pregnant. She expresses hope that Daigo will find a job of which their child can be proud. During the ensuing argument, Daigo receives a call for an encoffinment for Mrs Yamashita. Daigo prepares her body in front of both the Yamashita family and Mika, who had known the public bath owner. The ritual earns him the respect of all present, and Mika stops insisting that Daigo change jobs.
Sometime later, they learn of the death of Daigo's father. Daigo experiences renewed feelings of anger and tells the others at the NK office that he refuses to deal with his father's body. Feeling ashamed of having abandoned her own son long ago, Yuriko tells this to Daigo in an effort to change his mind. Daigo berates Yuriko and storms out before collecting himself and turning around. He goes with Mika to another village to see the body. Daigo is at first unable to recognize him, but takes offence when local funeral workers are careless with the body. He insists on dressing it himself, and while doing so finds a stone-letter that he had given to his father, held tight in the dead man's hands. The childhood memory of his father's face returns to him, and after he finishes the ceremony, Daigo gently presses the stone-letter to Mika's pregnant belly.
The film was created over a period of ten years, starting with the idea for the film by the main actor Masahiro Motoki himself. He learned to play the cello especially for the film and learned the art of burial with a real body washer. The director attended funerals to understand the feelings of the relatives. Since death and burial in Japan, on the one hand - as shown in the film - are ceremonial and, on the other hand, are taboo subjects in public, the director had initially not expected the film to be of great commercial success.